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European Journal of Human Genetics: EJHG

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https://www.readbyqxmd.com/read/28198392/coffee-consumption-is-associated-with-dna-methylation-levels-of-human-blood
#1
Yu-Hsuan Chuang, Austin Quach, Devin Absher, Themistocles Assimes, Steve Horvath, Beate Ritz
Beneficial health effects have been attributed to coffee consumption, but it is not yet known whether epigenetics may have a role in this process. Here we associate epigenome-wide DNA methylation levels to habitual coffee consumption from two studies with blood (2100 and 215 participants), and one with saliva samples (256 participants). Adjusting for age, gender, and blood cell composition, one CpG (cg21566642 near ALPPL2) surpassed genome-wide significance (P=3.7 × 10(-10)) and from among 10 additional CpGs significant at P≤5...
February 15, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28198391/mcm5-a-new-actor-in-the-link-between-dna-replication-and-meier-gorlin-syndrome
#2
Annalisa Vetro, Salvatore Savasta, Annalisa Russo Raucci, Cristina Cerqua, Geppo Sartori, Ivan Limongelli, Antonella Forlino, Silvia Maruelli, Paola Perucca, Debora Vergani, Giuliano Mazzini, Andrea Mattevi, Lucia Anna Stivala, Leonardo Salviati, Orsetta Zuffardi
Meier-Gorlin syndrome (MGORS) is a rare disorder characterized by primordial dwarfism, microtia, and patellar aplasia/hypoplasia. Recessive mutations in ORC1, ORC4, ORC6, CDT1, CDC6, and CDC45, encoding members of the pre-replication (pre-RC) and pre-initiation (pre-IC) complexes, and heterozygous mutations in GMNN, a regulator of cell-cycle progression and DNA replication, have already been associated with this condition. We performed whole-exome sequencing (WES) in a patient with a clinical diagnosis of MGORS and identified biallelic variants in MCM5...
February 15, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28176767/intragenic-fmr1-disease-causing-variants-a-significant-mutational-mechanism-leading-to-fragile-x-syndrome
#3
Angélique Quartier, Hélène Poquet, Brigitte Gilbert-Dussardier, Massimiliano Rossi, Anne-Sophie Casteleyn, Vincent des Portes, Claire Feger, Elsa Nourisson, Paul Kuentz, Claire Redin, Julien Thevenon, Anne-Laure Mosca-Boidron, Patrick Callier, Jean Muller, Gaetan Lesca, Frédéric Huet, Véronique Geoffroy, Salima El Chehadeh, Matthieu Jung, Benoit Trojak, Stéphanie Le Gras, Daphné Lehalle, Bernard Jost, Stéphanie Maury, Alice Masurel, Patrick Edery, Christel Thauvin-Robinet, Bénédicte Gérard, Jean-Louis Mandel, Laurence Faivre, Amélie Piton
Fragile-X syndrome (FXS) is a frequent genetic form of intellectual disability (ID). The main recurrent mutagenic mechanism causing FXS is the expansion of a CGG repeat sequence in the 5'-UTR of the FMR1 gene, therefore, routinely tested in ID patients. We report here three FMR1 intragenic pathogenic variants not affecting this sequence, identified using high-throughput sequencing (HTS): a previously reported hemizygous deletion encompassing the last exon of FMR1, too small to be detected by array-CGH and inducing decreased expression of a truncated form of FMRP protein, in three brothers with ID (family 1) and two splice variants in boys with sporadic ID: a de novo variant c...
February 8, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28176766/a-fast-and-accurate-method-for-detection-of-ibd-shared-haplotypes-in-genome-wide-snp-data
#4
Douglas W Bjelland, Uday Lingala, Piyush S Patel, Matt Jones, Matthew C Keller
Identical by descent (IBD) segments are used to understand a number of fundamental issues in genetics. IBD segments are typically detected using long stretches of identical alleles between haplotypes in phased, whole-genome SNP data. Phase or SNP call errors in genomic data can degrade accuracy of IBD detection and lead to false-positive/negative calls and to under/overextension of true IBD segments. Furthermore, the number of comparisons increases quadratically with sample size, requiring high computational efficiency...
February 8, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28176765/recontacting-in-clinical-genetics-and-genomic-medicine-we-need-to-talk-about-it
#5
Daniele Carrieri, Sandi Dheensa, Shane Doheny, Angus J Clarke, Peter D Turnpenny, Anneke M Lucassen, Susan E Kelly
No abstract text is available yet for this article.
February 8, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28145430/reconstructing-the-population-history-of-the-largest-tribe-of-india-the-dravidian-speaking-gond
#6
Gyaneshwer Chaubey, Rakesh Tamang, Erwan Pennarun, Pavan Dubey, Niraj Rai, Rakesh Kumar Upadhyay, Rajendra Prasad Meena, Jayanti R Patel, George van Driem, Kumarasamy Thangaraj, Mait Metspalu, Richard Villems
The Gond comprise the largest tribal group of India with a population exceeding 12 million. Linguistically, the Gond belong to the Gondi-Manda subgroup of the South Central branch of the Dravidian language family. Ethnographers, anthropologists and linguists entertain mutually incompatible hypotheses on their origin. Genetic studies of these people have thus far suffered from the low resolution of the genetic data or the limited number of samples. Therefore, to gain a more comprehensive view on ancient ancestry and genetic affinities of the Gond with the neighbouring populations speaking Indo-European, Dravidian and Austroasiatic languages, we have studied four geographically distinct groups of Gond using high-resolution data...
February 1, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28145429/securing-the-use-of-existing-sample-collections-for-future-human-genetic-research
#7
George Kanoungi, Peter Nürnberg, Michael Nothnagel
Hundreds of thousands of individuals have been genotyped in the past decades using genotyping arrays, representing both a valuable data resource for future biomedical research and a substantial investment in human genetic research. However, novel chip designs and their altered sets of single-nucleotide polymorphisms (SNPs) pose the question of how well established data resources, such as large samples of healthy controls genotyped on legacy arrays, can be combined with newer samples genotyped on those novel arrays using genotype imputation...
February 1, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28145428/collagen-synthesis-disruption-and-downregulation-of-core-elements-of-tgf-%C3%AE-hippo-and-wnt-pathways-in-keratoconus-corneas
#8
Michal Kabza, Justyna A Karolak, Malgorzata Rydzanicz, Michał W Szcześniak, Dorota M Nowak, Barbara Ginter-Matuszewska, Piotr Polakowski, Rafal Ploski, Jacek P Szaflik, Marzena Gajecka
To understand better the factors contributing to keratoconus (KTCN), we performed comprehensive transcriptome profiling of human KTCN corneas for the first time using an RNA-Seq approach. Twenty-five KTCN and 25 non-KTCN corneas were enrolled in this study. After RNA extraction, total RNA libraries were prepared and sequenced. The discovery RNA-Seq analysis (in eight KTCN and eight non-KTCN corneas) was conducted first, after which the replication RNA-Seq experiment was performed on a second set of samples (17 KTCN and 17 non-KTCN corneas)...
February 1, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28145427/variability-in-assigning-pathogenicity-to-incidental-findings-insights-from-ldlr-sequence-linked-to-the-electronic-health-record-in-1013-individuals
#9
Maya S Safarova, Eric W Klee, Linnea M Baudhuin, Erin M Winkler, Michelle L Kluge, Suzette J Bielinski, Janet E Olson, Iftikhar J Kullo
Knowledge of variant pathogenicity is key to implementing genomic medicine. We describe variability between expert reviewers in assigning pathogenicity to sequence variants in LDLR, the causal gene in the majority of cases of familial hypercholesterolemia. LDLR was sequenced on the Illumina HiSeq platform (average read depth >200 × ) in 1013 Mayo Biobank participants recruited from 2012 to 2013. Variants with a minor allele frequency (MAF) <5% predicted to be functional or referenced in HGMD (Human Gene Mutation Database) or NCBI-ClinVar databases were reviewed...
February 1, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28145426/two-novel-bmp-2-variants-identified-in-patients-with-thoracic-ossification-of-the-ligamentum-flavum
#10
Xiaochen Qu, Zhongqiang Chen, Dongwei Fan, Shen Xiang, Chuiguo Sun, Yan Zeng, Weishi Li, Zhaoqing Guo, Qiang Qi, Woquan Zhong, Yun Jiang
Thoracic ossification of the ligamentum flavum (TOLF)is a common cause of thoracic spinal canal stenosis and has been reported almost exclusively in East Asian countries. In this study, we established a relationship between bone morphogenic protein 2 (BMP-2) and TOLF. We divided patients into two groups according to severity of ossification and identified susceptible loci through exome sequencing. We identified 39 novel likely pathogenic variants in 29 genes in the transforming growth factor-beta (TGF-β) superfamily or TGF-β/BMPs signaling pathway, including two missense variants in BMP-2 (NM_001200...
February 1, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28145425/loss-of-function-of-kcnc1-is-associated-with-intellectual-disability-without-seizures
#11
Karine Poirier, Géraldine Viot, Laura Lombardi, Clémence Jauny, Pierre Billuart, Thierry Bienvenu
p.(Arg320His) mutation in the KCNC1 gene in human 11p15.1 has recently been identified in patients with progressive myoclonus epilepsies, a group of rare inherited disorders manifesting with action myoclonus, myoclonic epilepsy, and ataxia. This KCNC1 variant causes a dominant-negative effect. Here we describe three patients from the same family with intellectual disability and dysmorphic features. The three affected individuals carry a c.1015C>T (p.(Arg339*)) nonsense variant in KCNC1 gene. As previously observed in the mutant mouse carrying a disrupted KCNC1 gene, these findings reveal that individuals with a KCNC1 loss-of-function variant can present intellectual disability without seizure and epilepsy...
February 1, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28145424/whole-genome-view-of-the-consequences-of-a-population-bottleneck-using-2926-genome-sequences-from-finland-and-united-kingdom
#12
Himanshu Chheda, Priit Palta, Matti Pirinen, Shane McCarthy, Klaudia Walter, Seppo Koskinen, Veikko Salomaa, Mark Daly, Richard Durbin, Aarno Palotie, Tero Aittokallio, Samuli Ripatti
Isolated populations with enrichment of variants due to recent population bottlenecks provide a powerful resource for identifying disease-associated genetic variants and genes. As a model of an isolate population, we sequenced the genomes of 1463 Finnish individuals as part of the Sequencing Initiative Suomi (SISu) Project. We compared the genomic profiles of the 1463 Finns to a sample of 1463 British individuals that were sequenced in parallel as part of the UK10K Project. Whereas there were no major differences in the allele frequency of common variants, a significant depletion of variants in the rare frequency spectrum was observed in Finns when comparing the two populations...
February 1, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28145423/evaluation-of-copy-number-variants-as-modifiers-of-breast-and-ovarian-cancer-risk-for-brca1-pathogenic-variant-carriers
#13
Logan C Walker, Louise Marquart, John F Pearson, George A R Wiggins, Tracy A O'Mara, Michael T Parsons, Daniel Barrowdale, Lesley McGuffog, Joe Dennis, Javier Benitez, Thomas P Slavin, Paolo Radice, Debra Frost, Andrew K Godwin, Alfons Meindl, Rita Katharina Schmutzler, Claudine Isaacs, Beth N Peshkin, Trinidad Caldes, Frans Bl Hogervorst, Conxi Lazaro, Anna Jakubowska, Marco Montagna, Xiaoqing Chen, Kenneth Offit, Peter J Hulick, Irene L Andrulis, Annika Lindblom, Robert L Nussbaum, Katherine L Nathanson, Georgia Chenevix-Trench, Antonis C Antoniou, Fergus J Couch, Amanda B Spurdle
Genome-wide studies of patients carrying pathogenic variants (mutations) in BRCA1 or BRCA2 have reported strong associations between single-nucleotide polymorphisms (SNPs) and cancer risk. To conduct the first genome-wide association analysis of copy-number variants (CNVs) with breast or ovarian cancer risk in a cohort of 2500 BRCA1 pathogenic variant carriers, CNV discovery was performed using multiple calling algorithms and Illumina 610k SNP array data from a previously published genome-wide association study...
February 1, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28120840/non-invasive-prenatal-diagnosis-of-spinal-muscular-atrophy-by-relative-haplotype-dosage
#14
Michael Parks, Samantha Court, Benjamin Bowns, Siobhan Cleary, Samuel Clokie, Julie Hewitt, Denise Williams, Trevor Cole, Fiona MacDonald, Mike Griffiths, Stephanie Allen
Although technically possible, few clinical laboratories across the world have implemented non-invasive prenatal diagnosis (NIPD) for selected single-gene disorders, mostly owing to the elevated costs incurred. Having previously proven that NIPD for X-linked disorders can be feasibly implemented in clinical practice, we have now developed a test for the NIPD of an autosomal-recessive disorder, spinal muscular atrophy (SMA). Cell-free DNA was extracted from maternal blood and prepared for massively parallel sequencing on an Illumina MiSeq by targeted capture enrichment of single-nucleotide polymorphisms across a 6 Mb genomic window on chromosome 5 containing the SMN1 gene...
January 25, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28120839/signatures-of-human-european-palaeolithic-expansion-shown-by-resequencing-of-non-recombining-x-chromosome-segments
#15
Pierpaolo Maisano Delser, Rita Neumann, Stéphane Ballereau, Pille Hallast, Chiara Batini, Daniel Zadik, Mark A Jobling
Human genetic diversity in Europe has been extensively studied using uniparentally inherited sequences (mitochondrial DNA (mtDNA) and the Y chromosome), which reveal very different patterns indicating sex-specific demographic histories. The X chromosome, haploid in males and inherited twice as often from mothers as from fathers, could provide insights into past female behaviours, but has not been extensively investigated. Here, we use HapMap single-nucleotide polymorphism data to identify genome-wide segments of the X chromosome in which recombination is historically absent and mutations are likely to be the only source of genetic variation, referring to these as phylogeographically informative haplotypes on autosomes and X chromosome (PHAXs)...
January 25, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28120838/psychosocial-effects-in-parents-and-children-12-years-after-newborn-genetic-screening-for-type-1-diabetes
#16
Nicola J Kerruish, Dione M Healey, Andrew R Gray
Little is known about the psychosocial consequences of testing newborns for genetic susceptibility to multifactorial diseases. This study reports quantitative psychosocial evaluations of parents and children 12 years after screening for type 1 diabetes (T1D). Two parent-child cohorts participated: children at increased genetic risk of T1D and children at low genetic risk. T1D risk status was determined at birth as part of a prospective study investigating potential environmental triggers of autoimmunity. Parent measures included ratings of children's emotional, behavioural and social functioning (Child Behaviour Checklist) and parenting style (Alabama Parenting Questionnaire)...
January 25, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28120837/suggestive-association-between-variants-in-il1rapl-and-asthma-symptoms-in-latin-american-children
#17
Cintia Rodrigues Marques, Gustavo No Costa, Thiago Magalhães da Silva, Pablo Oliveira, Alvaro A Cruz, Neuza Maria Alcantara-Neves, Rosemeire L Fiaccone, Bernardo L Horta, Fernando Pires Hartwig, Esteban G Burchard, Maria Pino-Yanes, Laura C Rodrigues, Maria Fernanda Lima-Costa, Alexandre C Pereira, Mateus H Gouveia, Hanaisa P Sant Anna, Eduardo Tarazona-Santos, Maurício Lima Barreto, Camila Alexandrina Figueiredo
Several genome-wide association studies have been conducted to investigate the influence of genetic polymorphisms in the development of allergic diseases, but few of them have included the X chromosome. The aim of present study was to perform an X chromosome-wide association study (X-WAS) for asthma symptoms. The study included 1307 children of which 294 were asthma cases. DNA was genotyped using 2.5 HumanOmni Beadchip from Illumina. Statistical analyses were performed in PLINK 1.9, MACH 1.0 and Minimac2. The variant rs12007907 (g...
January 25, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28120836/from-exomes-to-genomes-challenges-and-solutions-in-population-based-genetic-association-studies
#18
Paul L Auer, Suzanne M Leal
No abstract text is available yet for this article.
January 25, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28098151/juvenile-myelomonocytic-leukemia-associated-variants-are-associated-with-neo-natal-lethal-noonan-syndrome
#19
Heather Mason-Suares, Diana Toledo, Jean Gekas, Katherine A Lafferty, Naomi Meeks, M Cristina Pacheco, David Sharpe, Thomas E Mullen, Matthew S Lebo
Gain-of-function variants in some RAS-MAPK pathway genes, including PTPN11 and NRAS, are associated with RASopathies and/or acquired hematological malignancies, most notably juvenile myelomonocytic leukemia (JMML). With rare exceptions, the spectrum of germline variants causing RASopathies does not overlap with the somatic variants identified in isolated JMML. Studies comparing these variants suggest a stronger gain-of-function activity in the JMML variants. As JMML variants have not been identified as germline defects and have a greater impact on protein function, it has been speculated that they would be embryonic lethal...
January 18, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28098150/a-survey-of-sub-saharan-gene-flow-into-the-mediterranean-at-risk-loci-for-coronary-artery-disease
#20
Miguel M Álvarez-Álvarez, Daniela Zanetti, Robert Carreras-Torres, Pedro Moral, Georgios Athanasiadis
This study tries to find detectable signals of gene flow of Sub-Saharan origin into the Mediterranean in four genomic regions previously associated with coronary artery disease. A total of 366 single-nucleotide polymorphisms were genotyped in 772 individuals from 10 Mediterranean countries. Population structure analyses were performed, in which a noticeable Sub-Saharan component was found in the studied samples. The overall percentage of this Sub-Saharan component presents differences between the two Mediterranean coasts...
January 18, 2017: European Journal of Human Genetics: EJHG
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